Analysing Viruses Using Advanced Mass Spectrometry Methods

Abstract

This thesis aims to highlight the beneficial use of mass spectrometry in the study of viruses. From complex characterisation of analytes and development of new MS instrumentation to address pharmaceutical questions, to high-throughput diagnostic assays of viral infection, MS can fulfil of all these experimental needs. Firstly, Chapter 2 explores the use ion mobility mass spectrometry to probe conformational heterogeneity of adeno-associated viruses. It is the first-known example of AAVs analysed with drift tube IMS, providing first principle calculated values for collisional cross sections. We also show travelling wave-IMS performing m/z separation, employing higher TW velocity and amplitude to move ions through the drift tube via their m/z rather than their mobility. Using both methods we investigate structural diversity in AAV capsids. Continuing the use of specialised MS technology to study viruses, Chapter 3 discusses the development of a novel charge-detection mass spectrometry instrument that has been used to analyse AAVs. The instrument comprises a new design, where ions are first passed through an Aerolens, achieving a steady-laminar subsonic flow profile, before being steered via hexapoles into the CDMS analyser. Here, the ions follow a figure of eight path and their time of flight and charge are measured. CDMS can handle mass heterogeneity in analytes such as AAVs due to measuring m/z and z directly, negating the need for charge state deconvolution to determine molecular weight. In Chapter 4, MS is shown to be vital in high-throughput methods to detect viruses, as exhibited with the pandemic-causing SARS-CoV-2 virus. This work outlines the development of a widely applicable proteomic assay for the detection of SARS-CoV-2 N peptides in patient swab and saliva samples. The study was a hugely collaborative effort conducted across academia, industry and medical services in the UK. Written in a protocol format, the manuscript presents a framework for potential development of other viral LCMS diagnostic assays that may be needed in the future.

Date of Award	1 Aug 2025
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Sabine Flitsch (Supervisor) & Perdita Barran (Supervisor)